Contents

Brain data

Brain data

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI

Code imports

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

--2022-05-26 15:55:44--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210726/neuromod-anat-brain-qmri.zip
Resolving github.com (github.com)... 140.82.113.3
Connecting to github.com (github.com)|140.82.113.3|:443... connected.
HTTP request sent, awaiting response... 

Archive:  neuromod-anat-brain-qmri.zip
  inflating: data/brain/results-neuromod-anat-brain-qmri.csv  
  inflating: data/brain/._results-neuromod-anat-brain-qmri.csv  
  inflating: data/brain/report-neuromod-anat-brain.html  
  inflating: data/brain/._report-neuromod-anat-brain.html  
  inflating: data/brain/neuromod-anat-brain.nextflow.log  
  inflating: data/brain/history-neuromod-anat-brain  
  inflating: data/brain/._history-neuromod-anat-brain  
  inflating: data/brain/timeline-neuromod-anat-brain.html  
  inflating: data/brain/._timeline-neuromod-anat-brain.html  

302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220526%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220526T155544Z&X-Amz-Expires=300&X-Amz-Signature=b9ba3cfed9ad29dab93905d8c12c01dd5f420abf1d89e2bde1d74ece5a915ea0&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream [following]
--2022-05-26 15:55:44--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220526%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220526T155544Z&X-Amz-Expires=300&X-Amz-Signature=b9ba3cfed9ad29dab93905d8c12c01dd5f420abf1d89e2bde1d74ece5a915ea0&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 939721 (918K) [application/octet-stream]
Saving to: ‘neuromod-anat-brain-qmri.zip’

     0K .......... .......... .......... .......... ..........  5% 5.45M 0s
    50K .......... .......... .......... .......... .......... 10% 6.69M 0s
   100K .......... .......... .......... .......... .......... 16% 23.5M 0s
   150K .......... .......... .......... .......... .......... 21% 34.6M 0s
   200K .......... .......... .......... .......... .......... 27% 10.2M 0s
   250K .......... .......... .......... .......... .......... 32% 32.8M 0s
   300K .......... .......... .......... .......... .......... 38% 33.0M 0s
   350K .......... .......... .......... .......... .......... 43% 31.2M 0s
   400K .......... .......... .......... .......... .......... 49% 67.0M 0s
   450K .......... .......... .......... .......... .......... 54% 17.2M 0s
   500K .......... .......... .......... .......... .......... 59%  115M 0s
   550K .......... .......... .......... .......... .......... 65% 32.7M 0s
   600K .......... .......... .......... .......... .......... 70% 39.0M 0s
   650K .......... .......... .......... .......... .......... 76% 93.4M 0s
   700K .......... .......... .......... .......... .......... 81%  129M 0s
   750K .......... .......... .......... .......... .......... 87% 56.1M 0s
   800K .......... .......... .......... .......... .......... 92%  137M 0s
   850K .......... .......... .......... .......... .......... 98%  135M 0s
   900K .......... .......                                    100%  143M=0.04s

2022-05-26 15:55:44 (23.3 MB/s) - ‘neuromod-anat-brain-qmri.zip’ saved [939721/939721]

Load data plot it

dataset.load()

fig_gm = Plot(dataset, plot_name = 'new-fig-2')

fig_gm.title = 'Brain gray matter qMRI microstructure'

fig_gm.display('jupyter-book', tissue = 'GM')

White matter qMRI

fig_wm = Plot(dataset, plot_name = 'new-fig-4')

fig_wm.title = 'Brain white matter qMRI microstructure'

fig_wm.display('jupyter-book', tissue = 'WM')

Spine

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

dataset.load()
dataset.data['T1w']

--2022-05-26 15:55:46--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.113.3
Connecting to github.com (github.com)|140.82.113.3|:443... connected.
HTTP request sent, awaiting response... 

302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220526%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220526T155546Z&X-Amz-Expires=300&X-Amz-Signature=1c6786c5bf39d39c5025bd45a615a6685bfe8bb3ea0862dea513e33cdddee387&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-05-26 15:55:46--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/9e444c00-c9e2-11eb-880c-f9aa2a43f100?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220526%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220526T155546Z&X-Amz-Expires=300&X-Amz-Signature=1c6786c5bf39d39c5025bd45a615a6685bfe8bb3ea0862dea513e33cdddee387&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19324 (19K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... ........                                   100% 18.4M=0.001s

2022-05-26 15:55:46 (18.4 MB/s) - ‘spinalcord_results.zip’ saved [19324/19324]

Archive:  spinalcord_results.zip
  inflating: data/spine/DWI_RD.csv   
  inflating: data/spine/DWI_FA.csv   
  inflating: data/spine/csa-SC_T2w.csv  
  inflating: data/spine/DWI_MD.csv   
  inflating: data/spine/MTR.csv      
  inflating: data/spine/MTsat.csv    
  inflating: data/spine/csa-GM_T2s.csv  
  inflating: data/spine/csa-SC_T1w.csv  
  inflating: data/spine/._csa-SC_T1w.csv  
  inflating: data/spine/T1.csv
Subject Session Timestamp SCT Version Filename Slice (I->S) VertLevel MEAN(area) STD(area) MEAN(angle_AP) ... STD(diameter_AP) MEAN(diameter_RL) STD(diameter_RL) MEAN(eccentricity) STD(eccentricity) MEAN(orientation) STD(orientation) MEAN(solidity) STD(solidity) SUM(length)
0 1 3 2021-06-09 23:24:08 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 51:93 2:3 64.109061 3.127582 -4.670983 ... 0.464761 10.640776 0.333651 0.690605 0.054994 3.202127 2.184708 0.976971 0.007494 34.565242
1 1 1 2021-06-09 23:24:10 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 31:75 2:3 67.680431 1.598728 -4.254822 ... 0.225578 10.843164 0.307774 0.680936 0.039585 2.149545 1.734302 0.980308 0.009615 36.167347
2 6 1 2021-06-09 23:24:11 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 45:81 2:3 62.953114 1.769023 -0.646246 ... 0.216321 11.513113 0.470660 0.792890 0.029588 1.260913 1.049494 0.965233 0.014776 30.644730
3 6 4 2021-06-09 23:24:12 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 58:95 2:3 63.925810 2.765595 -1.132526 ... 0.248317 11.727604 0.490648 0.803257 0.028672 1.754369 1.049329 0.971605 0.012450 31.247426
4 5 1 2021-06-09 23:24:18 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 19:57 2:3 53.010013 11.097434 -1.790824 ... 1.087683 10.965275 0.675722 0.822167 0.059414 4.036279 2.295310 0.952220 0.027352 33.355815
5 6 3 2021-06-09 23:24:19 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 38:75 2:3 62.990802 2.049191 -2.338349 ... 0.298265 11.506661 0.596266 0.792194 0.041279 1.614134 1.158783 0.973527 0.010495 31.364216
6 1 2 2021-06-09 23:24:19 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 47:86 2:3 67.511930 1.726861 -6.577358 ... 0.186145 10.874612 0.275935 0.690540 0.031751 2.855729 1.967201 0.977647 0.008612 32.528253
7 6 2 2021-06-09 23:24:21 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 89:125 2:3 64.823566 18.835219 13.113466 ... 1.159209 9.503113 2.506067 0.576338 0.152557 22.042768 32.322329 0.968538 0.032237 10.122137
8 2 1 2021-06-09 23:41:15 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 1:38 2:3 66.455289 4.204379 0.095829 ... 0.684070 11.992443 0.585042 0.794791 0.061804 2.234122 1.464966 0.963074 0.016533 31.424022
9 3 1 2021-06-09 23:41:20 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 51:85 2:3 59.927681 1.980624 -0.778617 ... 0.334499 10.086060 0.232852 0.658816 0.049798 2.475063 1.644264 0.972640 0.009458 28.297791
10 2 2 2021-06-09 23:41:24 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 12:50 2:3 73.688109 2.833139 -0.068322 ... 0.406465 12.065046 0.492764 0.756302 0.053939 2.367144 1.803792 0.966030 0.009791 32.356730
11 3 3 2021-06-09 23:41:39 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 43:77 2:3 60.621684 1.733616 -0.009478 ... 0.358365 10.632869 0.308162 0.726909 0.049649 1.681134 1.217510 0.970807 0.010769 28.389363
12 2 4 2021-06-09 23:41:39 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 9:46 2:3 69.405673 4.568637 -0.749008 ... 0.543059 12.227376 0.665839 0.796428 0.053488 2.145301 1.623586 0.958420 0.020529 31.442066
13 3 2 2021-06-09 23:41:42 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 33:66 2:3 60.228814 1.776652 -1.464265 ... 0.247391 10.486967 0.214164 0.716856 0.033921 1.850661 1.538691 0.966100 0.007298 27.236579
14 5 2 2021-06-09 23:41:45 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 44:82 2:3 64.717972 4.153035 -3.034680 ... 0.567947 11.448594 0.408139 0.769825 0.056204 4.103625 1.847953 0.966696 0.012619 32.529064
15 2 3 2021-06-09 23:50:43 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 3:39 2:3 73.905494 2.073274 -0.691532 ... 0.368828 12.371408 0.639116 0.780126 0.052688 1.694898 1.187327 0.963111 0.014391 30.534960
16 3 4 2021-06-09 23:55:17 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 40:74 2:3 59.915665 2.030933 -2.222570 ... 0.296578 10.445562 0.243935 0.716104 0.038919 2.551453 2.010580 0.972863 0.010084 28.329492
17 4 2 2021-06-09 23:55:38 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 49:84 2:3 59.717857 2.220913 2.572138 ... 0.399145 10.999128 0.354854 0.775108 0.045832 2.195005 1.555832 0.972639 0.015228 29.056988
18 4 3 2021-06-09 23:55:53 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 43:77 2:3 61.969221 2.026699 6.989458 ... 0.326731 10.956739 0.419218 0.753243 0.040568 2.095929 1.251544 0.976777 0.009427 28.313078

19 rows × 24 columns

dataset.data['T2w']
Subject Session Timestamp SCT Version Filename Slice (I->S) VertLevel MEAN(area) STD(area) MEAN(angle_AP) ... STD(diameter_AP) MEAN(diameter_RL) STD(diameter_RL) MEAN(eccentricity) STD(eccentricity) MEAN(orientation) STD(orientation) MEAN(solidity) STD(solidity) SUM(length)
0 1 3 2021-06-09 23:20:52 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 161:203 2:3 80.774162 3.246713 -3.760068 ... 0.174290 11.942165 0.386189 0.692055 0.028034 4.826952 2.124976 0.973148 0.006615 34.526392
1 1 1 2021-06-09 23:20:54 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 160:201 2:3 80.312877 1.602798 -3.958454 ... 0.148831 11.899994 0.348936 0.689786 0.032309 3.342223 1.895299 0.973535 0.009511 33.716889
2 6 1 2021-06-09 23:20:55 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 158:194 2:3 72.958267 2.394267 -0.230000 ... 0.206093 12.298752 0.455764 0.786437 0.025628 0.972269 0.813403 0.972373 0.010028 30.494727
3 6 4 2021-06-09 23:21:00 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 167:203 2:3 72.129244 2.513562 -2.145414 ... 0.180008 12.327045 0.417297 0.794967 0.019853 1.783156 0.920410 0.969491 0.009872 30.558270
4 1 2 2021-06-09 23:21:02 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 162:203 2:3 80.768423 1.967870 -5.074403 ... 0.180384 11.935064 0.352203 0.692630 0.031759 2.725679 1.980338 0.974296 0.007769 33.951292
5 5 1 2021-06-09 23:21:05 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 159:196 2:3 70.779953 4.773098 -1.899860 ... 0.773255 12.190368 0.565430 0.779750 0.071128 3.074997 1.954591 0.956469 0.019386 31.359579
6 6 3 2021-06-09 23:21:05 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 166:201 2:3 73.894805 2.227882 0.547178 ... 0.174199 12.449794 0.470167 0.792112 0.023507 1.604021 1.084022 0.967781 0.010371 29.962644
7 6 2 2021-06-09 23:21:12 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 164:200 2:3 73.129881 1.990473 -0.959923 ... 0.223915 12.384761 0.445033 0.792261 0.026887 1.640786 1.149530 0.970194 0.011049 30.874411
8 2 1 2021-06-09 23:38:23 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 157:193 2:3 92.724125 7.198446 -0.533592 ... 0.500942 13.469831 0.903365 0.749762 0.061652 3.007144 1.340842 0.970252 0.010245 31.142010
9 3 1 2021-06-09 23:38:25 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 141:177 2:3 73.617773 1.283275 -0.176559 ... 0.162039 11.618506 0.249626 0.719638 0.026723 1.350991 0.866047 0.970433 0.008960 29.966024
10 2 2 2021-06-09 23:38:28 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 156:191 2:3 94.587712 7.628431 -0.855157 ... 0.571808 13.618790 0.856929 0.751709 0.060540 2.065212 1.229055 0.970512 0.010239 30.640014
11 3 3 2021-06-09 23:38:40 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 161:196 2:3 70.593648 1.455799 -0.991364 ... 0.267249 11.246244 0.328627 0.702012 0.046127 1.260142 1.145153 0.970805 0.008657 29.249095
12 2 4 2021-06-09 23:38:42 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 160:193 2:3 93.571468 6.715923 -1.310382 ... 0.499746 13.510144 0.754180 0.750687 0.055164 1.432686 1.105488 0.970806 0.009661 28.757132
13 3 2 2021-06-09 23:38:46 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 162:198 2:3 72.980170 1.733563 -0.169089 ... 0.218192 11.669006 0.227977 0.728585 0.027002 1.021736 0.860224 0.971586 0.007557 29.619905
14 5 2 2021-06-09 23:38:47 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 154:191 2:3 74.857807 2.759146 -2.745917 ... 0.388765 12.401970 0.406430 0.775455 0.041603 2.156050 1.223840 0.966862 0.013124 31.380837
15 2 3 2021-06-09 23:48:42 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 159:193 2:3 92.666900 8.162162 -0.596256 ... 0.609800 13.567128 0.933170 0.758917 0.066758 1.366771 1.115320 0.969417 0.010025 29.350071
16 3 4 2021-06-09 23:53:25 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 158:194 2:3 71.268228 1.688296 0.149827 ... 0.272076 11.275181 0.260300 0.698106 0.041606 1.752418 1.216747 0.975077 0.009043 30.022830
17 4 2 2021-06-09 23:53:48 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 164:200 2:3 74.732375 0.995570 -0.057076 ... 0.173023 12.063074 0.345358 0.754853 0.027804 2.550164 1.247343 0.967420 0.011174 29.705806
18 4 3 2021-06-09 23:54:02 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 164:199 2:3 75.005645 0.909686 4.142686 ... 0.251494 11.967497 0.381923 0.743363 0.040588 1.571435 1.604254 0.972454 0.008886 28.928858

19 rows × 24 columns

previous

Results

next

Content with notebooks